Running Morpheus through R Statistics

[Эрвин Визард (Earvin Wizard)]

Dear colleagues,

Do we have possibility to start CPM calculations in Morpheus through R interface?

Other words, do Morpheus API available in R language?

Best wishes,

Ivan Azarov

[Lutz Brusch]

Hi Ivan,

there is no direct integration of Morpheus into R (yet) but you may invoke a simulation from R that runs outside of R and then you import results from the logger files do your statistics in R.

In R you would use

system2("morpheus /path/to/model.xml", arg)

where arg may provide options like "--outdir /path/to/results/dir" (that dir must have been created before) and/or "--set symbol_of_model_parameter=value" (e.g. "--set k1=0.01") to set model parameter values from within R.

(And the same strategy works from Python.)

Best,
Lutz

[Эрвин Визард (Earvin Wizard)]

Thank you, Lutz!

Very interesting. This option is something new for me...

суббота, 14 сентября 2024 г. в 00:28:44 UTC+3, Lutz Brusch:

[Эрвин Визард (Earvin Wizard)]

Dear Lutz,

In such case, what is the optimal way to perform simple version of Sensitivity Analysis for Cellular Potts models constructed in Morpheus?

суббота, 14 сентября 2024 г. в 12:24:04 UTC+3, Эрвин Визард (Earvin Wizard):

[Эрвин Визард (Earvin Wizard)]

Ok, question is solved: Parameter sweep was presented in manual.

понедельник, 14 октября 2024 г. в 13:43:50 UTC+3, Эрвин Визард (Earvin Wizard):